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mirror of https://github.com/QuantumPackage/qp2.git synced 2024-11-04 20:43:40 +01:00
qp2/src/nuclei/write_pt_charges.py
2023-02-23 16:38:40 +01:00

81 lines
2.0 KiB
Python

#!/usr/bin/env python
import os
import sys
# First argument is the EZFIO file
# It reads a file EZFIO_point_charges.xyz written in this way:
# charge x y z (Angstrom)
# for all charges
def zip_in_ezfio(ezfio,tmp):
tmpzip=tmp+".gz"
cmdzip="gzip -c "+tmp+" > "+tmpzip
os.system(cmdzip)
os.system("rm "+tmp)
cmdmv="mv "+tmpzip+" "+EZFIO+"/nuclei/"+tmpzip
os.system(cmdmv)
def mv_in_ezfio(ezfio,tmp):
cmdmv="mv "+tmp+" "+EZFIO+"/nuclei/"+tmp
os.system(cmdmv)
# Getting the EZFIO
EZFIO=sys.argv[1]
EZFIO=EZFIO.replace("/", "")
print(EZFIO)
# Reading the point charges and convert the Angstrom geometry in Bohr for QP
f = open(EZFIO+'_point_charges.xyz','r')
lines = f.readlines()
convert_angs_to_bohr=1.8897259885789233
n_charges=0
coord_x=[]
coord_y=[]
coord_z=[]
charges=[]
for line in lines:
data = line.split()
if(len(data)>0):
n_charges += 1
charges.append(str(data[0]))
coord_x.append(str(convert_angs_to_bohr*float(data[1])))
coord_y.append(str(convert_angs_to_bohr*float(data[2])))
coord_z.append(str(convert_angs_to_bohr*float(data[3])))
# Write the file containing the number of charges and set in EZFIO folder
tmp="n_pts_charge"
fncharges = open(tmp,'w')
fncharges.write(" "+str(n_charges)+'\n')
fncharges.close()
mv_in_ezfio(EZFIO,tmp)
# Write the file containing the charges and set in EZFIO folder
tmp="pts_charge_z"
fcharges = open(tmp,'w')
fcharges.write(" 1\n")
fcharges.write(" "+str(n_charges)+'\n')
for i in range(n_charges):
fcharges.write(charges[i]+'\n')
fcharges.close()
zip_in_ezfio(EZFIO,tmp)
# Write the file containing the charge coordinates and set in EZFIO folder
tmp="pts_charge_coord"
fcoord = open(tmp,'w')
fcoord.write(" 2\n")
fcoord.write(" "+str(n_charges)+' 3\n')
#fcoord.write(" "+' 3 '+str(n_charges)+' \n')
for i in range(n_charges):
fcoord.write(' '+coord_x[i]+'\n')
for i in range(n_charges):
fcoord.write(' '+coord_y[i]+'\n')
for i in range(n_charges):
fcoord.write(' '+coord_z[i]+'\n')
fcoord.close()
zip_in_ezfio(EZFIO,tmp)